Congrats on the new boat. Window leaks are common on our C&C's and there is a definate procedure for replacement. South Shore Yachst has a lot of the older C&C parts also.
As far as the pedestal leak, what exactly is leaking. Is the floor soft? This also goes for the decks. Our boats are alol blasa cored at least to the waterline, some all the way. If water intrudes it can wet and destroy the core requiring complete replacement of the area in the worst case scenario. First thing is to identify the area which is wet and also the reason. Then to see the level of repair. Some are easy quick fixes like drying out or digging out the core and refilling with epoxy. Some may require a cut out and reglassing, depends on how much the area is affected. Hopefullu you areas are not in load bearing areas such as chainplates.
In any event it is imperative that all thru deck/ hulkl ntrustions be checked and sealed corrrectly and maintain their integrity.
I also suggest you join the C&C owners group
C&C Yachts - C&C Photo Album & Resource Center
You have a great boat (obviously I am prejudiced as I own a C&C 35MKIII also)...fast and comfortable to cruise with and see was initially made well. It up to the owner to mainatain that. Post some pictures when you get a chance of her and affected areas.